Sandbox 4

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{{Seed}}
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[[Image:1emaBiomics4.gif|350 px]]
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[[Image:1tsj.png|left|200px]]
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The line below this paragraph, containing "STRUCTURE_1tsj", creates the "Structure Box" on the page.
 
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
 
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
 
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or leave the SCENE parameter empty for the default display.
 
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=Crystal structure of protein from Staphylococcus aureus=
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Green fluorescent protein ('''GFP'''), originally isolated from the jellyfish Aequorea victoria (PDB entry [[1ema]]), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.
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PDB entry 1tsj refers to a hypothetical protein of 139 residues which is a predicted dimer<ref> Henrick, K., and Thornton, J.M. (1998). PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23, 358- 361.</ref> and predicted as a cytoplasmic protein.<ref> Bhasin, M., Garg, A. and Raghava, GPS (2005) PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics. 21, 2522-2524.
 
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Gardy JL, Spencer C, Wang K, Ester M, Tusn?dy GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS. (2003) PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res. 31, 3613-3617.
 
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Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner. (2003). Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers. Bioinformatics. 20, 547-556.
 
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Hua S, Sun Z. (2001). Support vector machine approach for protein subcellular localization prediction. Bioinformatics. 17, 721-728.</ref>
 
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The protein is associated with Pfam<ref>Finn R, Griffiths-Jones S, Bateman A. (2003). Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. Chapter 2: Unit 2.5.</ref> entry PF06983 of 3-demethylubiquinone-9 3-methyltransferases.
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== Exploring the Structure ==
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<applet load='1ema' size='300' frame='true' align='right' caption='Insert caption here' />
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Among the sequence homologs found by PSI-Blast<ref> Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.</ref> there are the predicted 3-demethylubiquinone-9 3-methyltransferase proteins Q192X9 from Desulfitobacterium hafniense and A9VFW6 from Bacillus weihenstephanensis. Its potential substrate is S-adenosyl-L-methionine with the formal charge +1.
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GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The
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<scene name='Sandbox_4/Green_fp/1'>chromophore</scene>, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.<ref>PMID:8703075</ref>
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PDB entry [[2rk9]] was found to be structurally<ref> Arnold K, Kiefer F, Kopp J, Battey JN, Podvinec M, Westbrook JD, Berman HM, Bordoli L, Schwede T. (2008). The Protein Model Portal. J Struct Funct Genomics.</ref> similar to the query protein Q8NX24 and share a significant sequence similarity<ref> Emmert D.B., Stoehr P.J., Stoesser G., Cameron G.N. (1994). The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res. 26, 3445-3449.</ref> of 21.0%. This structure homolog is an Oxidoreductase from Vibrio Splendidus and binds methylglyoxal which is not charged. Another structural similarity was found with PDB entry [[1t47]] which is a 4-hydroxyphenylpyruvate dioxygenase, but the sequence similarity is lower (7.7%).
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[[Image:Chimera 1tsjA 2rk9B.png|thumb|350px|right|Superimposition between chain A of Q8NX24 (orange) and chain B of 2rk9 (green). The arrow indicates the active site of 2rk9.]]
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Both the sequence and structure homologs are from the same superfamily titled 'Glyoxalase/bleomycin resistance protein/dioxygenase'. The Superimposition<ref> Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.</ref> between chain A of Q8NX24 (orange) and chain B of 2rk9 (green) shows that the proteins indeed have similar folds.
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It seems that the chosen active site of Q8NX24 is the largest cavity found on the protein's surface, in most cases this cavity is the functional area.<ref> J. Liang, H. Edelsbrunner, and C. Woodward, (1998). Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7, 1884–1897.</ref> Evidence approving this choice is that the superimpositions with 2rk9 placed its known active site<ref> Thornalley P.J., (2003). Glyoxalase I – structure, function and a critical role in the enzymatic defence against glycation. Biochemical Soc Trans. 31, 1343-1348.</ref> at the same location.
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The electrostatic potential<ref>Sanner, M.F. (1999). Python: a programming language for software integration and development. J. Mol. Graph. Model. 17, 57-61.</ref> on the protein's surface is mostly negative.
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[[Image:Electrostatic potential 1tsj.PNG|thumb|350px|none|The electrostatic potential of Q8NX24. The figure was produced with Python Molecular Viewer.]]
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According to the evolutionary conservation<ref>Goldenberg O, Erez E, Nimrod G, Ben-Tal N. (2009). The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res. 37, D323-327.</ref> the potential catalytic area is <applet load='1tsj' size='400' frame='true' align='right' caption='1tsj, resolution 2.60Å' /> <scene name='1tsj/Evolutionary_consevation_1tsj/1'>highly preserved</scene> and negatively charged.
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<center>{{Template:ColorKey_ConSurf}}</center>
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The potential substrate S-adenosyl-L-methionine has positive formal charge which fits the negative electrostatic potential in the potential catalytic area. The alternative substrate found by the structural homology methylglyoxal is not charged and thus less probable to attach to the potential catalytic area.
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It seems more likely that Q8NX24 belongs to the Glyoxalase/bleomycin resistance protein/dioxygenase superfamily and functions as a demethylubiquinone-9 3-methyltransferase protein.
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==References==
==References==
<references/>
<references/>
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[[Category: Staphylococcus aureus subsp. aureus]]
 
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[[Category: Burley, S K.]]
 
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[[Category: Gorman, J.]]
 
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[[Category: Min, T.]]
 
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[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
 
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[[Category: Shapiro, L.]]
 
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[[Category: Conserved hypothetical protein]]
 
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[[Category: Crystal structure]]
 
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[[Category: New york structural genomics consortium]]
 
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[[Category: New york structural genomix research consortium]]
 
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[[Category: Nysgxrc]]
 
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[[Category: Protein structure initiative]]
 
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[[Category: Psi]]
 
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[[Category: Structural genomic]]
 

Current revision


Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.


Exploring the Structure

Insert caption here

Drag the structure with the mouse to rotate

GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The , responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]


References

  1. ↑ Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ. Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996 Sep 6;273(5280):1392-5. PMID:8703075
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